Owing to the massive amount of data accumulated through various genome-wide sequencing and gene expression projects, there is an urgent need to develop novel tools to uncover the functions of each gene in human genome. Functional genomics studies will speed up the discovery and validation of drug targets, and open avenues for new concepts in drug therapy and diagnostics of complex human diseases. Recent innovations in gene knockdown technology based on small interfering RNA (siRNA) have revolutionized gene functional analysis. The ultimate goal of the proposed project is to develop and make commercially available a set of libraries expressing small interfering RNA (siRNA) against all characterized human, mouse and rat genes. Phase I of this program will cover development of technology for construction of high complexity siRNA library of 8,500 characterized human genes in retroviral vector and testing functional performance of this library by isolation of biologically active cones using apoptosis modulation as a model. An important technical aspect of the proposed technology is its integration with the Affymetrix GeneChip technology that would allow to use the power and speed of microarray analysis that is already broadly available for academic and industrial research for functional gene discovery purposes. At the Phase II, the program will be extended towards development and commercialization of a set of human, mouse and rat whole-genome siRNA libraries. siRNA libraries will allow to perform global search for functional genes involved in a variety of diseases and to validate new drug targets by arbitrary selective inactivation of specific mRNAs and corresponding proteins in the context of the living cells. The established technology will be applied, in collaboration with Cleveland Clinic Foundation, to drug target discovery in prostate cancer. The anticipated outcomes of the proposed research will be a commercially available set of kits for high-throughput gene functional analysis and validated anticancer drug targets for treatment of prostate cancer.